Alzheimer's disease is associated with the abnormal deposits of amyloid beta protein (Ab) that occurs as fibrils within the cerebral neuropil. To characterize the way in which these fibrils assemble under different pH conditions, we have performed transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) on synthetic full-length Ab peptides as well as various Ab peptides with truncated sequences. TEM images of negatively stained preparations provide information about the fibril width and morphology, whereas STEM analysis of rapidly frozen, unstained preparations provides a quantitative determination of the mass-per-length (MPL) and thus the numbers of beta-sheets within fibrils. Taken together the results reveal how the structure of fibrils grown from Alzheimer-related Ab peptides depend on the growth conditions, including protein concentration and pH. MPL measurements reveal the existence of fundamental fibrillizing units, or "protofilaments", consisting of well-defined numbers of cross-beta sheets. Variations in fibril morphology at the EM level are being used by scientists in NIDDK to correlate with atomic-level information about the peptide backbone conformation obtained from NMR spectroscopy.